Extrachromosomal DNA (ecDNA) drives hepatocellular carcinoma malignancy through high-copy amplification of chromosome 1q21-derived PIP5K1A oncogene.

Extrachromosomal circular DNA (eccDNA) drives oncogene amplification in multiple malignancies, yet its landscape and clinical relevance in hepatocellular carcinoma (HCC) remain poorly characterized. Here, we performed Circle-seq and RNA-seq on six pairs of HCC tumors and adjacent non-tumor tissues, identifying a 3 Mb extrachromosomal DNA (ecDNA) from chromosome 1q21 in 50 % tumor samples. This ecDNA contained multiple genes, but functional analysis prioritized PIP5K1A due to its central role in PI3K/AKT signaling and association with poor prognosis. The extrachromosomal localization of PIP5K1A was validated through outward PCR, inward PCR, Sanger sequencing, and fluorescence in situ hybridization (FISH) assays. Kaplan-Meier (KM) analysis demonstrated that elevated PIP5K1A expression was associated with an unfavorable prognosis in patients with HCC. In vivo and in vitro assays revealed that ecDNA-driven PIP5K1A amplification enhanced HCC proliferation, migration, and apoptosis resistance. Our study provides a genome-wide eccDNA profiling of HCC, implicating 1q21 ecDNA and PIP5K1A as prognostic markers and therapeutic targets, offering insights into HCC treatment strategies.